VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2009 - 00:31:01 CDT

Raluca,
  I see a number of strange things going on in your script:
1) Why do you have all of the "menu" commands? These should probably
   all be deleted, there's no reason to be manipulating the GUIs from
   within your script, it's just slowing things down.

2) Another odd thing is the code that you have that's overwriting
   $tmpFile (same filename you just read in!) with another copy.
   I don't understand the point of the "work pqr file" section...

Please delete all of the menu commands and explain or fix the
weird code in the "work pqr file" section, and send me your cleaned
up version, and we'll go from there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 31, 2009 at 09:57:56AM +0200, Raluca Mihaela ANDREI wrote:
> Hi,
> sorry for the unclear message, when I talked about threads, I
> was meaning asynchronous operations, and the question was
> about the mol command.
> As you asked, I send to you on the following my script code:
>
> # VMD for LINUX, version 1.8.6 (March 18, 2009)
>
> set chan [open "input.txt"]
> gets $chan inputdir
> gets $chan workdir
> gets $chan filename
> gets $chan num
> close $chan
>
> for {set x 1} {$x<=$num} {incr x} {
>
> #--- PQR file loading
> menu files off
> menu files on
> animate style Loop
> display resetview
>
> set tmpFile $inputdir$filename$x.pqr
> mol new $tmpFile type {pqr} first 0 last -1 step 1 waitfor 1
> animate style Loop
> menu files off
> #--------------------
>
> #--- Work PQR file
> menu apbsrun off
> menu apbsrun on
>
> set tmpFile $workdir$filename$x.pqr
> animate write pqr $tmpFile beg 0 end 0 skip 1 $x-1)
> #--------------------
>
> #--- POT.DX file creation
> set potname pot
> set potFile $workdir$potname.dx
> display resetview
> mol addfile $potFile type {dx} first 0 last -1 step 1 waitfor
> 1 $x-1
> animate style Loop
> menu apbsrun off
> #--------------------
>
> #--- Rename DX file
> set tmpFile $workdir$filename$x.dx
> file copy -force $potFile $tmpFile
> file delete $potFile
> #--------------------
>
> #--- Rendering (OBJ file creation)
> menu graphics off
> menu graphics on
> mol modstyle 0 0 Surf 1.400000 0.000000
> menu graphics off
> axes location Off
> menu render off
> menu render on
> set tmpFile $workdir$filename$x.obj
> render Wavefront $tmpFile true
> menu render off
> #--------------------
>
> }
>
> # VMD for LINUX, version 1.8.6 (March 18, 2009)
> # end of log file.
>
> Thank you very much.
> Regards,
>
> Raluca
>
>
> On Sat, 28 Mar 2009 14:41:52 -0500
> John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Hi,
> > It's not clear to me what you're talking about when you
> >refer to "thread" in the context of your script. The VMD
> >command interpreter is single-threaded, although some
> >operations
> >are asynchronous by default (e.g. 'mol new', etc).
> >
> >Please send a copy of your script, as the single command you
> >included below is insufficient to indicate the source of
> >your
> >problem.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Fri, Mar 27, 2009 at 06:44:32PM +0100, Raluca Mihaela
> >ANDREI wrote:
> >>Hi,
> >>I have to load different PQR files, and for each one I have
> >>to
> >>create the relevant pot.dx file and the relevant rendering
> >>file.
> >>
> >>I would have to carry out these operations automatically by
> >>running a tcl script, so I would include all relevant
> >>statements in a "for" cycle.
> >>
> >>But I have a problem when the script runs the "mol" command
> >>as
> >>the following:
> >>
> >>"mol addfile $potFile type {dx} first 0 last -1 step 1
> >>waitfor
> >>-1 $molID"
> >>
> >>After this statement, a different thread creating the pot.dx
> >>file runs, while the script continues to run the other
> >>statements, without waiting for the end of the previous one.
> >>
> >>Is it possible, to wait for the end of the thread relevant
> >>the
> >>pot.dx creation, and to execute the other statements just
> >>when
> >>the pot.dx creation is finished?
> >>
> >>Thank you.
> >>
> >>Raluca
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078